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- PDB-8ytg: Crystal structures of human IRF2BP2 RING domain in complex with I... -

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Basic information

Entry
Database: PDB / ID: 8ytg
TitleCrystal structures of human IRF2BP2 RING domain in complex with IRF2 peptide
Components
  • Interferon regulatory factor 2
  • Interferon regulatory factor 2-binding protein 2
KeywordsTRANSCRIPTION / IRF2BP2 / RING domain / IRF2
Function / homology
Function and homology information


immature B cell differentiation / immune system process / Pyroptosis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription corepressor activity / Interferon gamma signaling / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription activator activity, RNA polymerase II-specific ...immature B cell differentiation / immune system process / Pyroptosis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription corepressor activity / Interferon gamma signaling / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / focal adhesion / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Interferon regulatory factor 2-binding protein 1 & 2, zinc finger / Interferon regulatory factor 2-binding protein 1/2, C3HC4-type RING finger superfamily / Interferon regulatory factor 2-binding protein zinc finger / Interferon regulatory factor-1/2 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. ...Interferon regulatory factor 2-binding protein 1 & 2, zinc finger / Interferon regulatory factor 2-binding protein 1/2, C3HC4-type RING finger superfamily / Interferon regulatory factor 2-binding protein zinc finger / Interferon regulatory factor-1/2 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Interferon regulatory factor 2 / Interferon regulatory factor 2-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWang, G.C. / Ding, J.P.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030305 China
CitationJournal: To Be Published
Title: IRF2BP2 recognizes and bind to a conserved RxSVI sequence motif of protein partners and interacts with ZBTB16 to regulate megakaryocytic differentiation
Authors: Wang, G.C. / Ding, J.P.
History
DepositionMar 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon regulatory factor 2-binding protein 2
B: Interferon regulatory factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9685
Polymers9,7722
Non-polymers1963
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-37 kcal/mol
Surface area5060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.733, 39.868, 36.247
Angle α, β, γ (deg.)90.00, 108.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interferon regulatory factor 2-binding protein 2 / IRF-2-binding protein 2 / IRF-2BP2


Mass: 8867.110 Da / Num. of mol.: 1 / Fragment: RING domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF2BP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z5L9
#2: Protein/peptide Interferon regulatory factor 2 / IRF-2


Mass: 905.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P14316
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.5 M ammonium sulfate and 0.1 M sodium acetate (pH 4.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.45→39.87 Å / Num. obs: 12812 / % possible obs: 98.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 10.3
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1270

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→34.43 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 625 4.89 %
Rwork0.1649 --
obs0.1661 12782 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms621 0 3 158 782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006636
X-RAY DIFFRACTIONf_angle_d0.873860
X-RAY DIFFRACTIONf_dihedral_angle_d5.31185
X-RAY DIFFRACTIONf_chiral_restr0.09394
X-RAY DIFFRACTIONf_plane_restr0.01112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.60.20071700.17033010X-RAY DIFFRACTION99
1.6-1.830.17551630.15163035X-RAY DIFFRACTION100
1.83-2.30.19761510.1663059X-RAY DIFFRACTION99
2.3-34.430.18421410.16773053X-RAY DIFFRACTION97

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